For me, Mega Man 2 has the best soundtrack of all time. Actraiser was great as well. That was my first experience with Yuzo Koshiro. I think that Contra has great music. I particularly like the Snow Field level. Can't really think of anything else that particularly sticks out. Castlevania is great. I really liked Duck Tales' music. There is probably better music, but it probably came from a game that I never played. All of Mega Man 2's music is great though, so that gets my vote.
EDIT: I also really liked the elevator-musicy vibe of Pilotwings' music. F-Zero had great music as well. I should also mention that I had a Super Nintendo back in the day so I don't know too much about the Genesis games' music. It is likely that there was better music on that platform than what I mentioned above.